We start with a couple of definitions: the genome is the ensemble of genes in an organism, and genomics is the study of the genome. The major goal of genomics is to determine the function of each gene in the genome, i e annotate the sequence. This is sometimes called functional genomics. Figure 12.1 gives an outline of the topic. The starting point is the gene; we shall not deal with gene mapping, since it is already well covered in genetics textbooks. We shall view the primary experimental data of genomics as the actual nucleotide sequence, and reiterate that genomics could simply be viewed as the study of the nonrandomness of DNA sequences.
KeywordsDynamic Programming Algorithm Unknown Sequence Symbol Transition Protein Function Prediction Longe Common Subsequence
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- 1.This procedure may yield a preparation containing RNA as well as DNA, bu1t RNA binds preferentially to boronate and thus can be separated from DNA.Google Scholar
- 2.In this context, `vector’ is used in the sense of vehicle.Google Scholar
- 3.This is somewhat related to Kruskal’s multidimensional scaling (MD-SCAL) analysis.Google Scholar
- 4.Unambiguously assembled nonoverlapping sequences are called `contigs’.Google Scholar
- 5.See Franca et al. for a review, and Braslaysky et al. for a recent single molecule technique.Google Scholar
- 6.In this context, `library’ is used merely to denote `collection’.Google Scholar
- 7.Note that `homology’ is defined as `similarity in structure of an organ or molecule, reflecting a common evolutionary origin’. Sequence similarity is insufficient to establish homology, since genomes contain both orthologous (related via common descent) and paralogous (resulting from duplications within the genome) genes.Google Scholar
- 8.The sentence, whose origin I forbear to reveal, goes on with “—hence its tremendous popularity.”Google Scholar
- 9.This is obtained by considering the number of ways of intercalating two sequences while preserving the order of symbols in each.Google Scholar
- 10.For example, BLOSUM50, a 20 x 20 score matrix (histidine scores 10 if replacing histidine, glutamine zero, and alanine —3, and so on). The diagonal terms are not equal.Google Scholar
- 11.Allison et al.Google Scholar
- 12.The concept of phylogeny was introduced by E. Haeckel.Google Scholar
- 13.rRNA has been championed by C. Woese.Google Scholar